is there any way to fix node sparkles without nodes showing up?
Now I see a lot of sparkles without nodes (ground lvl)
Also, recyclers are missing on airfield and satelite on my server, and some iron radtown shacks seems to be invissible. Their doors and barricades still show up (removed that with "ent kill"
Removed flying nodes and trees with the Rust Admin tool.

You really, really should've wiped your server after the hotfix came out last week.
To spawn a recycler, you can point where you want it, and type: spawn recycler , in the F1 console.

I have not wiped as well. I only had one player that build in the tunnels and his base is still underwater as a result, but the rest of the players was fine so we decided not to wipe.
Every Time you do a resource reset the sparkles stay. i have a fucktun of them on my map currently but it doesn't bother people. Remove all the resources and restart your server. Just refill all resources if nothing spawned after the restart.